Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Nature Microbiology

Volumn 1, Issue 4, 2016, Pages

  Weill, François Xavier ^a,p   Njamkepo, Elisabeth ^a   Fawal, Nizar ^a   Tran Dien, Alicia ^a   Hawkey, Jane ^b,c,d   Strockbine, Nancy ^e   Jenkins, Claire ^f   Talukder, Kaisar A ^g   Bercion, Raymond ^h,i   Kuleshov, Konstantin ^j   Kolínská, Renáta ^k   Russell, Julie E ^f   Kaftyreva, Lidia ^l   Accou Demartin, Marie ^a   Karas, Andreas ^m   Vandenberg, Olivier ^n,o   Mather, Alison E ^p,q   Mason, Carl J ^r   Page, Andrew J ^p   Ramamurthy, Thandavarayan ^s   Bizet, Chantal ^a   Gamian, Andrzej ^t   Carle, Isabelle ^a   Sow, Amy Gassama ⁱ   Bouchier, Christiane ^a   Wester, Astrid Louise ^u   Lejay Collin, Monique ^a   Fonkoua, Marie Christine ^v   Le Hello, Simon ^a   Blaser, Martin J ^w   Jernberg, Cecilia ^x   Ruckly, Corinne ^a   Mérens, Audrey ^y   Page, Anne Laure ^z   Aslett, Martin ^p   Roggentin, Peter ^aa   Fruth, Angelika ^ab   Denamur, Erick ^ac   Venkatesan, Malabi ^ad   Bercovier, Hervé ^ae   Bodhidatta, Ladaporn ^r   Chiou, Chien Shun ^af   Clermont, Dominique ^a   Colonna, Bianca ^ag   Egorova, Svetlana ^l   Pazhani, Gururaja P ^s   Ezernitchi, Analia V ^ah   Guigon, Ghislaine ^a   Harris, Simon R ^p   Izumiya, Hidemasa ^ai   Korzeniowska Kowal, Agnieszka ^t   Lutyhska, Anna ^aj   Gouali, Malika ^a   Grimont, Francine ^a   Langendorf, Céline ^z   Marejková, Monika ^k   Peterson, Lorea A M ^ak   Perez Perez, Guillermo ^w   Ngandjio, Antoinette ^v   Podkolzin, Alexander ^j   Souche, Erika ^a   Makarova, Mariia ^l   Shipulin, German A ^j   Ye, Changyun ^al   Žemličková, Helena ^k,am   Herpay, Mária ^an   Grimont, Patrick A D ^a   Parkhill, Julian ^p   Sansonetti, Philippe ^a   Holt, Kathryn E ^a   Brisse, Sylvain ^a,ao   Thomson, Nicholas R ^p,ap   more..

^a INSTITUT PASTEUR   (France)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^f PUBLIC HEALTH ENGLAND   (United Kingdom)

^g INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

^h INSTITUT PASTEUR DE BANGUI   (Central African Republic)

ⁱ INSTITUT PASTEUR DE DAKAR   (Senegal)

^j CENTRAL RESEARCH INSTITUTE OF EPIDEMIOLOGY   (Russian Federation)

^k NATIONAL INSTITUTE OF PUBLIC HEALTH   (Czech Republic)

^l ST PETERSBURG PASTEUR INSTITUTE   (Russian Federation)

^m UNIVERSITY OF KWAZULU NATAL   (South Africa)

ⁿ UNIVERSITY HOSPITAL BRUSSELS   (Belgium)

^o UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^p WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^q UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^r ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^s NATIONAL INSTITUTE OF CHOLERA AND ENTERIC DISEASES   (India)

^t INSTITUTE OF IMMUNOLOGY AND EXPERIMENTAL THERAPY   (Poland)

^u NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

^v CENTRE PASTEUR DU CAMEROUN   (Cameroon)

^w NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^x SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^y SERVICE D ENDOCRINOLOGIE   (France)

^z EPICENTRE   (France)

^aa Dr Brill Partner GmbH Institute for Hygiene and Microbiology   (Germany)

^ab ROBERT KOCH INSTITUTE   (Germany)

^ac INSERM   (France)

^ad WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^ae HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^af CENTER FOR DISEASE CONTROL   (Taiwan)

^ag SAPIENZA UNIVERSITY OF ROME   (Italy)

^ah MINISTRY OF HEALTH   (Israel)

^ai NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

^aj NATIONAL INSTITUTE OF HYGIENE   (Poland)

^ak PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^al National Institute for Communicable Disease Control and Prevention   (China)

^am CHARLES UNIVERSITY   (Czech Republic)

^an NATIONAL CENTER FOR EPIDEMIOLOGY   (Hungary)

^ao CNRS   (France)

^ap LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; GENETICS; GLOBAL HEALTH; HISTORY; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; PHYLOGEOGRAPHY; SEROTYPE; SHIGELLA DYSENTERIAE; SHIGELLOSIS;

DRUG RESISTANCE, BACTERIAL; DYSENTERY, BACILLARY; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; GLOBAL HEALTH; HISTORY, 19TH CENTURY; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; HUMANS; MOLECULAR EPIDEMIOLOGY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; SEROGROUP; SHIGELLA DYSENTERIAE;

EID: 85014542270     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/NMICROBIOL.2016.27     Document Type: Article

References (63)

1. Kohn, G. C. (ed.) Encyclopedia of Plague and Pestilence (Facts on File New York, 1995).
2. Rohmer, L. et al. Genomic analysis of the emergence of 20th century epidemic dysentery. BMC Genomics 15, 355 (2014).
3. Castenbrandt, H. K. A forgotten plague: dysentery in Sweden, 1750-1900. Scand. J. Hist. 39, 612-639 (2014).
4. Creighton, C. A History of Epidemics in Britain. Volume II: from the Extinction of Plague to the Present Time (Cambridge Univ. Press, 1894).
5. Shiga, K. Ueber den erreger der dysenterie in Japan. Vorläufige mitteilung. Zentralbl. Bakteriol. Microbiol. Hyg. 23, 599-600 (1898).
6. Manson-Bahr, P. H. Dysentery and diarrhoea in wartime. Br. Med. J. 2, 346-348 (1942).
7. Ledingham, J. C. & Penfold, W. J. Recent bacteriological experiences with typhoidal disease and dysentery. Br. Med. J. 2, 704-711 (1915).
8. Tribondeau, L. & Fichet, M. Note sur les dysenteries des Dardanelles. Ann. Inst. Pasteur (Paris) 30, 357-362 (1916).
9. Pupo, G. M., Lan, R. & Reeves, P. R. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl Acad. Sci. USA 97, 10567-10572 (2000).
10. Mata, L. J., and Gangarosa., E. J., Cáceres, A., Perera, D. R. & Mejicanos, M. L. Epidemic Shiga bacillus dysentery in Central America. I. Etiologic investigations in Guatemala, 1969. J. Infect. Dis. 122, 170-180 (1970).
11. Parsonnet, J. et al. Shigella dysenteriae type 1 infections in US travellers to Mexico, 1988. Lancet 2, 543-545 (1989).
12. Cobra, C. & Sack, D. A. The Control of Epidemic Dysentery in Africa: Overview, Recommendations, and Checklists (SD Publication Series, Technical Paper No. 27 (USAID, Bureau for Africa, Office of Sustainable Development, 1996); http://pdf.usaid.gov/pdf-docs/pnaby890.pdf
13. Rahaman, M. M., and Khan., M. M., Aziz, K. M., Islam, M. S. & Kibriya, A. K. An outbreak of dysentery caused by Shigella dysenteriae type 1 on a coral island in the Bay of Bengal. J. Infect. Dis. 132, 15-19 (1975).
14. Taylor, D. N. et al. Introduction and spread of multi-resistant Shigella dysenteriae 1 in Thailand. Am. J. Trop. Med. Hyg. 40, 77-85 (1989).
15. Murray, G. R. E. More on bacterial longevity: the Murray collection. ASM News 51, 261-262 (1985).
16. Baker, K. S. et al. The Murray collection of pre-antibiotic era Enterobacteriaceae: a unique research resource. Genome Med. 7, 97 (2015).
17. Yang, F. et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33, 6445-6458 (2005).
18. Vongsawan, A. A. et al. The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis. FEMS Microbiol. Lett. 362, pii: fnv011 (2015).
19. McKenzie, R. et al. Safety and immunogenicity of WRSd1, a live attenuated Shigella dysenteriae type 1 vaccine candidate. Vaccine 26, 3291-3296 (2008).
20. Launay, O. et al. Safety and immunogenicity of SC599, an oral live attenuated Shigella dysenteriae type-1 vaccine in healthy volunteers: results of a phase 2, randomized, double-blind placebo-controlled trial. Vaccine 27, 1184-1191 (2009).
21. Shiga, K. Observations on the epidemiology of dysentery in Japan. Philipp. J. Sci. 1, 485-500 (1906).
22. Holt, K. E. et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genet. 44, 1056-1059 (2012).
23. Robic, J. Une épidémie de dysenterie bacillaire à Madagascar (1927-1928). Bull. Soc. Path. Exot. 21, 709-713 (1928).
24. Guerin, P. J., and Grais., R. F., Rottingen, J. A. & Valleron, A. J. & Shigella Study Group. Using European travellers as an early alert to detect emerging pathogens in countries with limited laboratory resources. BMC Public Health 7, 8 (2007).
25. Bercion, R. et al. Molecular epidemiology of multidrug-resistant Shigella dysenteriae type 1 causing dysentery outbreaks in Central African Republic, 2003-2004. Trans R. Soc. Trop. Med. Hyg. 100, 1151-1158 (2006).
26. Luck, S. N., and Turner., S. A., Rajakumar, K., Sakellaris, H. & Adler, B. Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes. Infect. Immun. 69, 6012-6021 (2001).
27. Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462-465 (2011).
28. Wong, V. K. et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature Genet. 47, 632-639 (2015).
29. Islam, M. S. et al. Microbiological investigation of diarrhoea epidemics among Rwandan refugees in Zaire. Trans. R. Soc. Trop. Med. Hyg. 89, 506 (1995).
30. Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597-602 (2010).
31. Murray, E. G. D. An attempt at classification of Bacillus dysenteriae, based upon an examination of the agglutinating properties of fifty-three strains. J. R. Army Med. Corps 31, 257-271 (1918).
32. Langendorf, C. et al. Enteric bacterial pathogens in children with diarrhea in Niger: diversity and antimicrobial resistance. PLoS ONE 10, e0120275 (2015).
33. Taddei, F., Matic, I. & Radman, M. cAMP-dependent SOS induction and mutagenesis in resting bacterial populations. Proc. Natl Acad. Sci. USA 92, 11736-11740 (1995).
34. Picard, B. et al. Mutator natural Escherichia coli isolates have an unusual virulence phenotype. Infect. Immun. 69, 9-14 (2001).
35. Grimont, F. & Grimont, P. A. D. Determination of rDNA gene restriction patterns. Methods Mol. Biol. 46, 181-200 (1995).
36. Wirth, T. et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60, 1136-1151 (2006).
37. CTX-M-15 in Salmonella enterica serotype Concord isolates from internationally adopted children. Antimicrob. Agents Chemother. 53, 1808-1816 (2009).
38. Turner, S. A., and Luck., S. N., Sakellaris, H., Rajakumar, K. & Adler, B. Molecular epidemiology of the SRL pathogenicity island. Antimicrob. Agents Chemother. 47, 727-734 (2003).
39. Carattoli, A. et al. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63, 219-228 (2005).
40. Aziz, R. K. et al. The RAST server: rapid annotation using subsystems technology. BMC Genomics 9, 75 (2008).
41. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
42. Boetzer, M., and Henkel., C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578-579 (2011).
43. Boetzer, M. & Pirovano, W. Toward almost closed genomes with GapFiller. Genome Biol. 13, R56 (2012).
44. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
45. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
46. Carver, T. et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24, 2672-2676 (2008).
47. Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).
48. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729 (2013).
49. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128 (2007).
50. Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).
51. Cheng, L., and Connor., T. R., Siren, J., Aanensen, D. M. & Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224-1228 (2013).
52. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).
53. Connor, T. R. et al. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 4, e07335 (2015).
54. Baele, G. et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 29, 2157-2167 (2012).
55. Baele, G., and Li., W. L., Drummond, A. J., Suchard, M. A. & Lemey, P. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 30, 239-243 (2013).
56. Prosperi, M. C. et al. A novel methodology for large-scale phylogeny partition. Nature Commun. 2, 321 (2011).
57. Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640-2644 (2012).
58. Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895-3903 (2014).
59. García-Fernández, A. et al. Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. J. Antimicrob. Chemother. 61, 1229-1233 (2008).
60. García-Fernández, A. et al. Multilocus sequence typing of IncN plasmids. J. Antimicrob. Chemother. 66, 1987-1991 (2011).
61. Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691-3693 (2015).
62. Mitchell, A. et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213-D221 (2015).
63. Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 43, D1049-D1056 (2015).